MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Batch Index Model Treatment region Data Path
1 C6_PLX_01 C6 PLX region_0 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101
1 APP_PLX_01 APP PLX region_1 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101
1 APP_Ct_01 APP control region_2 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101
1 C6_Ct_01 C6 control region_3 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101
2 C6_PLX_02 C6 PLX region_0 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201
2 C6_Ct_02 C6 control region_1 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201
2 APP_Ct_02 APP control region_2 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201
2 APP_PLX_02 APP PLX region_3 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201

1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing

2.1 Cell Segmentation & Quality Control

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 146720 cells across 8 samples. Each sample cell count is shown in table following.

Segmented Cell Count in each Samples
Sample Index Cell Count
C6_PLX_02 31075
C6_Ct_02 26774
APP_Ct_02 24938
APP_PLX_02 18323
C6_Ct_01 14779
APP_PLX_01 11965
C6_PLX_01 10576
APP_Ct_01 8290
Transcript Count level Violin

Transcript Count level Violin

Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

2.2 Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

Umap of cells and colored by batch

Umap of cells and colored by batch

Umap of cells on each batch

Umap of cells on each batch

Leiden Umap clusters

Leiden Umap clusters

3. Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

Leiden Umap can be dividied to 28 clusters

Leiden Umap can be dividied to 28 clusters

3.1 Cell Annotation (Low resolution class)

MapMyCell Annotation Cell Count (Low resolution class)
class_name count
14 31 OPC-Oligo 31113
1 01 IT-ET Glut 29120
15 30 Astro-Epen 22524
10 33 Vascular 9681
27 18 TH Glut 7692
2 02 NP-CT-L6b Glut 7239
0 09 CNU-LGE GABA 6424
9 34 Immune 4272
16 12 HY GABA 3442
6 20 MB GABA 2853
5 11 CNU-HYa GABA 2291
4 07 CTX-MGE GABA 2216
8 27 MY GABA 2081
3 10 LSX GABA 1784
7 06 CTX-CGE GABA 1720
30 14 HY Glut 1539
12 19 MB Glut 1351
19 13 CNU-HYa Glut 1204
28 23 P Glut 1068
33 17 MH-LH Glut 1018
11 26 P GABA 1010
18 32 OEC 928
20 24 MY Glut 796
13 05 OB-IMN GABA 795
21 08 CNU-MGE GABA 604
23 04 DG-IMN Glut 499
31 16 HY MM Glut 466
17 29 CB Glut 379
25 28 CB GABA 158
29 21 MB Dopa 139
24 22 MB-HB Sero 138
26 03 OB-CR Glut 104
22 25 Pineal Glut 56
32 15 HY Gnrh1 Glut 16

3.2 Cell Annotation (High resolution subclass)

MapMyCell Annotation Cell Count (High resolution subclass)
subclass_name count
43 327 Oligo NN 29245
52 319 Astro-TE NN 8078
154 151 TH Prkcd Grin2c Glut 5919
124 333 Endo NN 5644
102 318 Astro-NT NN 5425
44 321 Astroependymal NN 5252
6 006 L4/5 IT CTX Glut 5233
16 009 L2/3 IT PIR-ENTl Glut 4415
2 030 L6 CT CTX Glut 4119
80 062 STR D2 Gaba 2982
5 004 L6 IT CTX Glut 2895
27 016 CA1-ProS Glut 2548
89 334 Microglia NN 2357
55 017 CA3 Glut 2268
76 331 Peri NN 1912
93 061 STR D1 Gaba 1894
142 326 OPC NN 1868
35 005 L5 IT CTX Glut 1621
10 007 L2/3 IT CTX Glut 1607
115 323 Ependymal NN 1522
135 325 CHOR NN 1444
17 014 LA-BLA-BMA-PA Glut 1347
28 338 Lymphoid NN 1307
1 022 L5 ET CTX Glut 1219
4 001 CLA-EPd-CTX Car3 Glut 1111
31 330 VLMC NN 1095
8 052 Pvalb Gaba 1087
168 154 PF Fzd5 Glut 1075
19 029 L6b CTX Glut 1057
69 012 MEA Slc17a7 Glut 1006
54 328 OEC NN 928
49 093 RT-ZI Gnb3 Gaba 899
71 101 ZI Pax6 Gaba 836
32 053 Sst Gaba 833
37 332 SMC NN 825
14 046 Vip Gaba 761
66 064 STR-PAL Chst9 Gaba 730
240 145 MH Tac2 Glut 699
7 069 LSX Nkx2-1 Gaba 697
100 063 STR D1 Sema5a Gaba 636
3 027 L6b EPd Glut 630
36 032 L5 NP CTX Glut 604
15 013 COAp Grxcr2 Glut 604
26 003 L5/6 IT TPE-ENT Glut 582
23 337 DC NN 507
57 010 IT AON-TT-DP Glut 504
12 002 IT EP-CLA Glut 498
98 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 494
22 049 Lamp5 Gaba 489
11 028 L6b/CT ENT Glut 486
97 037 DG Glut 479
141 025 CA2-FC-IG Glut 463
61 285 MY Lhx1 Gly-Gaba 462
48 070 LSX Prdm12 Slit2 Gaba 454
204 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 451
128 113 MEA-COA-BMA Ccdc42 Glut 410
91 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 357
59 114 COAa-PAA-MEA Barhl2 Glut 355
29 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 355
82 041 OB-in Frmd7 Gaba 329
209 146 LH Pou4f1 Sox1 Glut 319
127 073 MEA-BST Sox6 Gaba 315
63 020 L2/3 IT RSP Glut 306
21 304 NTS-PARN Neurod2 Gly-Gaba 305
119 079 CEA-BST Six3 Cyp26b1 Gaba 301
33 202 PRT Tcf7l2 Gaba 283
232 134 PH-ant-LHA Otp Bsx Glut 277
79 076 MEA-BST Lhx6 Nfib Gaba 271
56 047 Sncg Gaba 269
200 235 PG-TRN-LRN Fat2 Glut 264
18 071 LSX Prdm12 Zeb2 Gaba 264
249 129 VMH Nr5a1 Glut 263
90 320 Astro-OLF NN 260
222 104 TU-ARH Otp Six6 Gaba 255
30 201 PAG-RN Nkx2-2 Otx1 Gaba 254
189 217 PB Lmx1a Glut 252
149 098 AHN-SBPV-PVHd Pdrm12 Gaba 250
123 102 DMH-LHA Gsx1 Gaba 250
215 143 MM-ant Foxb1 Glut 249
176 317 Astro-CB NN 247
88 322 Tanycyte NN 241
263 149 PVT-PT Ntrk1 Glut 233
24 019 L2/3 IT PPP Glut 229
184 141 PH-SUM Foxa1 Glut 227
96 198 IC Six3 En2 Gaba 217
190 144 MM Foxb1 Glut 217
110 329 ABC NN 205
122 210 PRT Mecom Gaba 204
205 119 SI-MA-LPO-LHA Skor1 Glut 203
58 068 LSX Otx2 Gaba 203
9 090 BST-MPN Six3 Nrgn Gaba 202
39 048 RHP-COA Ndnf Gaba 201
53 315 DCO UBC Glut 197
174 152 RE-Xi Nox4 Glut 196
77 199 PAG-MRN-RN Foxa2 Gaba 194
170 089 PVR Six3 Sox3 Gaba 190
109 054 STR Prox1 Lhx6 Gaba 187
158 107 DMH Hmx2 Gaba 185
68 039 OB Meis2 Thsd7b Gaba 185
147 314 CB Granule Glut 182
103 082 CEA-BST Ebf1 Pdyn Gaba 177
25 018 L2 IT PPP-APr Glut 173
112 238 NTS Phox2b Glut 168
41 033 NP SUB Glut 162
106 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 159
62 200 PAG-ND-PCG Onecut1 Gaba 157
191 222 PB Evx2 Glut 156
73 051 Pvalb chandelier Gaba 155
157 074 MEA-BST Lhx6 Sp9 Gaba 152
196 057 NDB-SI-MA-STRv Lhx8 Gaba 149
45 278 NLL Gata3 Gly-Gaba 149
144 080 CEA-AAA-BST Six3 Sp9 Gaba 146
78 277 DTN-LDT-IPN Otp Pax3 Gaba 145
187 243 PGRN-PARN-MDRN Hoxb5 Glut 145
46 050 Lamp5 Lhx6 Gaba 141
75 023 SUB-ProS Glut 139
179 215 SNc-VTA-RAmb Foxa1 Dopa 139
121 216 MB-MY Tph2 Glut-Sero 138
64 103 PVHd-DMH Lhx6 Gaba 132
181 108 ARH-PVp Tbx3 Gaba 126
120 251 NTS Dbh Glut 125
99 045 OB-STR-CTX Inh IMN 123
47 195 SNr-VTA Pax5 Npas1 Gaba 119
84 056 Sst Chodl Gaba 119
218 221 LDT-PCG Vsx2 Lhx4 Glut 117
175 181 IC Tfap2d Maf Glut 116
172 147 AD Serpinb7 Glut 112
34 265 PB Sst Gly-Gaba 112
233 088 BST Tac2 Gaba 111
87 072 LSX Sall3 Lmo1 Gaba 111
257 150 CM-IAD-CL-PCN Sema5b Glut 108
150 021 L4 RSP-ACA Glut 104
105 058 PAL-STR Gaba-Chol 103
67 034 NP PPP Glut 103
164 224 PCG-PRNr Vsx2 Nkx6-1 Glut 102
95 264 PRNc Otp Gly-Gaba 98
13 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 98
116 081 ACB-BST-FS D1 Gaba 96
111 196 PAG-PPN Pax5 Sox21 Gaba 96
188 205 SC-PAG Lef1 Emx2 Gaba 92
20 008 L2/3 IT ENT Glut 91
152 036 HPF CR Glut 87
223 132 AHN-RCH-LHA Otp Fezf1 Glut 87
72 011 L2 IT ENT-po Glut 87
0 065 IA Mgp Gaba 86
50 283 PRP Otp Gly-Gaba 86
108 213 SCsg Gabrr2 Gaba 86
255 173 PAG Pou4f2 Glut 84
272 167 PRC-PAG Tcf7l2 Irx2 Glut 81
40 075 MEA-BST Lhx6 Nr2e1 Gaba 80
70 270 LDT-DTN Gata3 Nfix Gaba 80
185 263 CS-RPO Meis2 Gaba 79
60 031 CT SUB Glut 78
234 206 SCm-PAG Cdh23 Gaba 75
195 135 STN-PSTN Pitx2 Glut 75
220 133 PVH-SO-PVa Otp Glut 74
156 109 LGv-ZI Otx2 Gaba 74
166 100 AHN Onecut3 Gaba 73
148 267 CS-PRNr-PCG Tmem163 Otp Gaba 73
125 085 SI-MPO-LPO Lhx8 Gaba 73
118 271 NI-RPO Gata3 Nr4a2 Gaba 70
65 192 PPN-CUN-PCG Otp En1 Gaba 69
252 123 DMH Nkx2-4 Glut 69
138 313 CBX Purkinje Gaba 69
173 208 SC Lef1 Otx2 Gaba 68
207 139 PH-LHA Foxb1 Glut 67
42 042 OB-out Frmd7 Gaba 67
133 106 PVpo-VMPO-MPN Hmx2 Gaba 66
155 059 GPe-SI Sox6 Cyp26b1 Gaba 63
315 138 PH Pitx2 Glut 63
243 127 DMH-LHA Vgll2 Glut 59
101 043 OB-mi Frmd7 Gaba 59
153 335 BAM NN 58
94 262 Pineal Crx Glut 56
266 105 TMd-DMH Foxd2 Gaba 56
194 245 SPVI-SPVC Tlx3 Ebf3 Glut 56
247 125 DMH Hmx2 Glut 56
137 197 SNr Six3 Gaba 56
129 067 LSX Sall3 Pax6 Gaba 55
146 099 SBPV-PVa Six6 Satb2 Gaba 55
256 097 PVHd-SBPV Six3 Prox1 Gaba 53
159 182 CUN-PPN Evx2 Meis2 Glut 51
291 155 PRC-PAG Pax6 Glut 50
145 268 CS-PRNr-DR En1 Sox2 Gaba 50
113 246 CU-ECU-SPVI Foxb1 Glut 49
126 209 SCs Pax7 Nfia Gaba 49
92 015 ENTmv-PA-COAp Glut 48
177 299 MARN-PPY Ngfr Gly-Gaba 48
38 174 PAG Pou4f2 Mesi2 Glut 48
211 086 MPO-ADP Lhx8 Gaba 48
278 177 SCig-an-PPT Foxb1 Glut 48
313 120 MEA Otp Foxp2 Glut 48
271 124 MPN-MPO-PVpo Hmx2 Glut 48
107 055 STR Lhx8 Gaba 46
219 162 CUN Evx2 Lhx2 Glut 45
214 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 44
151 293 PAS-MV Ebf2 Gly-Gaba 44
239 164 APN C1ql4 Glut 44
246 092 TMv-PMv Tbx3 Hist-Gaba 43
136 207 SCs Dmbx1 Gaba 43
51 336 Monocytes NN 43
192 248 MV-SPIV Zic4 Neurod2 Glut 43
169 193 MRN-PPN-CUN Pax8 Gaba 43
251 128 VMH Fezf1 Glut 43
182 290 MY Prox1 Lmo7 Gly-Gaba 42
183 286 PPY-PGRNl Vip Glyc-Gaba 40
161 214 IPN Otp Crisp1 Gaba 38
167 204 SC Otx2 Gcnt4 Gaba 37
180 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba 37
83 261 HB Calcb Chol 36
74 254 VCO Mafa Meis2 Glut 36
269 094 SCH Six6 Cdc14a Gaba 36
258 308 DCO Il22 Gly-Gaba 36
290 228 PSV Pvalb Lhx2 Glut 34
237 130 LHA Pmch Glut 33
259 172 PAG Pou4f1 Ebf2 Glut 33
117 060 OT D3 Folh1 Gaba 33
213 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 33
143 272 LDT-PCG-CS Gata3 Lhx1 Gaba 33
285 160 PAG-SC Neurod2 Meis2 Glut 32
163 303 IRN Dmbx1 Pax2 Gly-Gaba 32
284 121 MEA-BST Otp Zic2 Glut 31
104 282 POR Spp1 Gly-Gaba 30
282 111 TRS-BAC Sln Glut 30
283 316 Bergmann NN 30
279 148 AV Col27a1 Glut 30
206 083 CEA-BST Rai14 Pdyn Crh Gaba 30
134 191 PAG-MRN Rln3 Gaba 29
254 212 SCs Lef1 Gli3 Gaba 29
298 066 NDB-SI-ant Prdm12 Gaba 28
216 159 IF-RL-CLI-PAG Foxa1 Glut 28
131 276 LDT-PCG St18 Gaba 27
235 115 MS-SF Bsx Glut 27
276 137 PH-an Pitx2 Glut 25
193 309 CB PLI Gly-Gaba 25
288 091 ARH-PVi Six6 Dopa-Gaba 25
186 324 Hypendymal NN 25
244 170 PAG-MRN Tfap2b Glut 25
130 044 OB Dopa-Gaba 24
268 180 SCiw Pitx2 Glut 23
132 257 SPVC Ccdc172 Glut 23
178 095 DMH Prdm13 Gaba 23
86 211 SC Tnnt1 Gli3 Gaba 23
197 279 PSV Pax2 Gly-Gaba 23
286 226 PRNc-PARN Tlx1 Glut 23
229 117 LHA Barhl2 Glut 22
228 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut 21
250 126 ARH-PVp Tbx3 Glut 20
308 026 NLOT Rho Glut 20
302 038 DG-PIR Ex IMN 20
289 131 LHA-AHN-PVH Otp Trh Glut 20
264 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba 20
296 156 MB-ant-ve Dmrta2 Glut 20
241 118 ADP-MPO Trp73 Glut 19
217 165 PAG-MRN Pou3f1 Glut 19
262 153 MG-POL-SGN Nts Glut 19
231 171 PAG Pou4f1 Bnc2 Glut 19
270 116 AVPV-MEPO-SFO Tbr1 Glut 18
293 122 LHA-MEA Otp Glut 18
292 169 PAG-SC Pou4f1 Zic1 Glut 18
236 140 PMd-LHA Foxb1 Glut 18
140 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba 18
198 163 APN C1ql2 Glut 17
238 296 RPA Pax6 Hoxb5 Gly-Gaba 17
160 231 IPN-LDT Vsx2 Nkx6-1 Glut 17
225 035 OB Eomes Ms4a15 Glut 17
199 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut 17
139 256 SPVC Mafa Glut 17
208 142 HY Gnrh1 Glut 16
212 237 PRP-NI-PRNc-GRN Otp Glut 16
267 176 SCig Foxb1 Glut 16
314 077 CEA-BST Gal Avp Gaba 15
309 112 GPi Tbr1 Cngb3 Gaba-Glut 15
224 136 PMv-TMv Pitx2 Glut 15
227 275 PDTg Otp Olig3 Gaba 14
210 310 CBX Golgi Gly-Gaba 14
81 302 MV Xdh Gly-Gaba 14
295 244 MV-SPIV Slc6a2 Glut 13
277 184 PAG Tcf24 Glut 13
171 273 PDTg-PCG Pax6 Gaba 12
261 175 SC Bnc2 Glut 12
317 190 ND-INC Foxd2 Glut 10
85 298 PRP Gata3 Slc6a5 Gly-Gaba 10
287 307 RO-RPA Pkd2l1 Gaba 10
242 295 CBN Dmbx1 Gaba 10
165 078 SI-MA-ACB Ebf1 Bnc2 Gaba 10
253 232 LDT Vsx2 Nkx6-1 Nfib Glut 9
275 312 CBX MLI Cdh22 Gaba 9
319 253 IO Fgl2 Glut 9
203 258 SPVC Nmu Glut 9
273 220 PB Pax5 Glut 9
201 255 SPVO Mafa Meis2 Glut 9
305 084 BST-SI-AAA Six3 Slc22a3 Gaba 9
310 187 SCsg Pde5a Glut 9
265 223 B-PB Nr4a2 Glut 9
297 166 MRN Pou3f1 C1ql4 Glut 8
248 110 BST-po Iigp1 Glut 8
230 252 DMX VII Tbx20 Chol 8
114 297 CU-ECU Pax2 Gly-Gaba 8
226 281 POR Gata3 Gly-Gaba 8
221 040 OB Trdn Gaba 8
162 178 SCig Foxb1 Otx2 Glut 8
320 250 CBN Neurod2 Pvalb Glut 7
294 179 SCdg-PAG Tfap2b Glut 7
260 234 MEV Ppp1r1c Glut 6
202 289 MDRNd Prox1 Pax6 Gly-Gaba 5
306 311 CBX MLI Megf11 Gaba 5
321 161 PAG Pou4f3 Glut 5
300 233 NLL-SOC Spp1 Glut 5
303 269 LDT Fgf7 Gaba 5
281 096 PVHd Gsc Gaba 5
245 239 MARN-GRN Pyy Glut 3
304 230 PRNr Otp Nfib Glut 3
301 249 NTS Aldh1a2 Glut 3
312 188 SCop Sln Glut 2
311 274 PDTg Otp Shroom3 Gaba 2
299 024 L5 PPP Glut 2
280 236 IRN Vip Glut 2
318 288 MDRN Hoxb5 Ebf2 Gly-Gaba 2
274 158 MRN-PAG Nkx6-1 Glut 2
307 294 MV Pax6 Gly-Gaba 2
322 218 PSV Lmx1a Trpv6 Glut 2
325 301 MV Nr4a2 Gly-Gaba 1
326 186 SCop Pou4f2 Neurod2 Glut 1
316 292 MV Nkx6-1 Gly-Gaba 1
324 227 PB-PSV Phox2b Glut 1
323 240 MDRNv Lhx4 Qrfprl Glut 1
327 260 MDRNv Crp Glut 1

3.3 Custome-selected cell type

To ensure accuracy, we exclude cells that are identified by map my cell but have less than 1% distribution in Leiden clusters. In this way, Additionally, we select specific target cell types and an appropriate resolution level that is suitable for our research purposes.

Custome cell type count
APP_Ct_01 APP_Ct_02 APP_PLX_01 APP_PLX_02 C6_Ct_01 C6_Ct_02 C6_PLX_01 C6_PLX_02
Astrocyte 591 3131 805 2501 983 4358 361 5726
CA1-ProS Glut 190 577 56 252 336 295 207 575
CA2 Glut 45 89 31 49 61 57 28 89
CA3 Glut 78 347 67 330 246 240 195 701
DG Glut 12 131 13 84 36 66 27 118
Endo 114 1337 111 939 247 1059 58 1710
HY GABA 139 459 539 448 450 540 314 381
HY Glut 76 131 135 261 178 328 157 664
L2 Glut 27 23 56 17 47 23 30 28
L2/3 Glut 516 1257 880 351 922 1046 535 939
L4 Glut 16 8 14 5 4 45 5 1
L4/5 Glut 590 707 1042 529 940 445 484 296
L5 Glut 423 385 480 240 550 443 474 267
L5/6 Glut 76 49 66 27 94 81 89 84
L6 Glut 316 311 390 259 470 355 366 324
L6b Glut 487 869 614 709 729 891 812 886
MB GABA 168 430 323 312 262 580 254 457
MB Glut 35 140 63 276 69 348 76 293
Microglia 201 699 19 2 243 1086 1 15
OPC 102 448 22 153 274 526 26 266
Oligo 913 5146 1255 4213 1688 6049 1251 7360
STR D1 GABA 172 500 604 351 258 321 191 101
STR D2 GABA 205 525 516 540 349 460 278 50
SUB-Pros Glut 13 13 16 4 9 63 10 9
TH Glut 473 1302 344 1192 1160 949 840 1317
VLMC 48 136 23 130 78 156 25 459

3.4 Scaled Cell Count heatmap

Cell Proportion Heatmap

Cell Proportion Heatmap

4. Spatial Visualization

4.1 Neurons

4.2 Non-Neurons

4.3 Microglia Gene Markers

5. Hippocampal Region Selection

5.1 Hippocampal Region Cell Count

Cell Selection Count in Hippocampal Region
Counts
APP_Ct_01 3880
APP_Ct_02 3241
APP_PLX_01 2305
APP_PLX_02 1959
C6_Ct_01 5786
C6_Ct_02 3350
C6_PLX_01 3363
C6_PLX_02 4418

5.2 Hippocampal Spatial Visualization

6. Gene differentiation

6.1 Hippocampal

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

6.1.1 APP only, PLX v.s. control

Cell number compare: ‘PLX’: 4264 ; ‘Control’: 7121

## [1] 4264
## [1] 7121

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
470 Csf1r -9.992595 -8.497447 0.0000000 0.0000000
466 App -9.321175 -7.206883 0.0000000 0.0000000
459 Selplg -8.342670 -6.263949 0.0000000 0.0000000
467 Ctss -9.638645 -5.085486 0.0000000 0.0000000
441 C1qa -6.676291 -5.084176 0.0000000 0.0000000
434 Tmem119 -5.920957 -4.544962 0.0000000 0.0000000
6 Penk 7.467743 4.347895 0.0000000 0.0000000
4 Adora2a 8.577372 3.707588 0.0000000 0.0000000
442 Inpp5d -6.713989 -3.474978 0.0000000 0.0000000
488 Egr1 -12.467212 -3.430572 0.0000000 0.0000000
427 Cx3cr1 -5.433567 -3.349348 0.0000001 0.0000003
498 Slc17a7 -18.380058 -3.326372 0.0000000 0.0000000
10 Ppp1r1b 5.211143 2.990984 0.0000002 0.0000011
457 Grin1 -8.249740 -2.755692 0.0000000 0.0000000
348 Itgam -2.424661 -2.656466 0.0153227 0.0445427
9 Drd2 5.634256 2.620728 0.0000000 0.0000001
387 Siglech -3.582790 -2.600245 0.0003399 0.0013075
482 Dnm1 -11.955046 -2.572117 0.0000000 0.0000000
476 Syp -10.921723 -2.533255 0.0000000 0.0000000
5 Six3 7.919350 2.530318 0.0000000 0.0000000
480 Apoe -11.712777 -2.436881 0.0000000 0.0000000
1 Syndig1l 11.199730 2.429623 0.0000000 0.0000000
411 Trem2 -4.667787 -2.339870 0.0000030 0.0000148
391 Plp1 -3.813616 2.281649 0.0001369 0.0005434
11 Otof 4.848666 2.204886 0.0000012 0.0000066
499 Camk2a -19.099926 -2.200464 0.0000000 0.0000000
495 Arc -15.471355 -2.044732 0.0000000 0.0000000
485 Vgf -12.289746 -2.035441 0.0000000 0.0000000
496 Dkk3 -15.656831 -2.028133 0.0000000 0.0000000
492 Syngap1 -14.241967 -1.949083 0.0000000 0.0000000
2 C4b 10.918763 1.898962 0.0000000 0.0000000
14 Scn4b 4.658997 1.884755 0.0000032 0.0000153
0 Gfap 17.104430 1.747727 0.0000000 0.0000000
493 Dlg4 -14.311377 -1.746045 0.0000000 0.0000000
468 Ptpru -9.713569 -1.710330 0.0000000 0.0000000
373 P2ry12 -3.117066 -1.664990 0.0018266 0.0063424
483 Cx3cl1 -12.080276 -1.662768 0.0000000 0.0000000
431 Nptx2 -5.712518 -1.612757 0.0000000 0.0000001
430 Cckbr -5.684848 -1.510544 0.0000000 0.0000001
453 Grin2a -7.467175 -1.499516 0.0000000 0.0000000
376 Gria1 -3.156925 -1.480083 0.0015944 0.0056540
461 Epha10 -8.605890 -1.440944 0.0000000 0.0000000
491 Syn1 -13.488163 -1.440494 0.0000000 0.0000000
350 Rspo1 -2.483363 -1.434904 0.0130148 0.0385054
494 Bin1 -14.323399 -1.424151 0.0000000 0.0000000
436 Gm2115 -6.024242 -1.398714 0.0000000 0.0000000
455 Nptx1 -7.868817 -1.389696 0.0000000 0.0000000
481 Nr4a1 -11.898462 -1.382180 0.0000000 0.0000000
465 Bcan -9.280068 -1.340949 0.0000000 0.0000000
497 Sorl1 -16.587605 -1.336206 0.0000000 0.0000000
489 Cck -12.516647 -1.297370 0.0000000 0.0000000
421 Ptk2b -5.111560 -1.292715 0.0000003 0.0000018
361 Abi3 -2.818073 -1.290162 0.0048313 0.0153862
478 Rph3a -11.049101 -1.284928 0.0000000 0.0000000
484 Mapt -12.197148 -1.249153 0.0000000 0.0000000
413 Plcxd2 -4.711940 -1.229122 0.0000025 0.0000123
490 Lynx1 -13.287546 -1.228083 0.0000000 0.0000000
379 Plcg2 -3.369969 -1.222410 0.0007518 0.0027238
419 Adrb1 -4.862046 -1.209240 0.0000012 0.0000063
13 Drd1 4.707247 1.205178 0.0000025 0.0000124
8 Meis2 6.155312 1.198299 0.0000000 0.0000000
447 Nr4a2 -7.062252 -1.190020 0.0000000 0.0000000
352 Ace -2.492969 -1.163853 0.0126680 0.0379395
450 Eno2 -7.358470 -1.162827 0.0000000 0.0000000
486 Slc30a3 -12.291239 -1.149618 0.0000000 0.0000000
18 Clic6 2.492862 -1.145236 0.0126718 0.0379395
460 Brinp1 -8.353975 -1.138802 0.0000000 0.0000000
456 Zbtb20 -8.184727 -1.123504 0.0000000 0.0000000
382 Olig1 -3.428355 -1.115202 0.0006073 0.0022491
479 Nptxr -11.069632 -1.105270 0.0000000 0.0000000
443 Fibcd1 -6.756305 -1.102211 0.0000000 0.0000000
414 Grin2b -4.727474 -1.049061 0.0000023 0.0000115
403 Kcnh7 -4.342469 -1.021783 0.0000141 0.0000629
358 Htr1a -2.690160 -1.021183 0.0071418 0.0223181
364 Celsr1 -2.878600 -1.013014 0.0039944 0.0129186
463 Fam131a -9.033947 -1.009017 0.0000000 0.0000000

6.1.2 C6 only, PLX v.s. control

Cell number compare: ‘PLX’: 7781 ; ‘Control’: 9136

## [1] 7781
## [1] 9136

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
2 App 12.126558 7.122068 0.0000000 0.0000000
497 Csf1r -11.103088 -5.479664 0.0000000 0.0000000
496 Selplg -9.522469 -5.325641 0.0000000 0.0000000
474 Clic6 -2.712040 -4.972346 0.0066871 0.0288235
499 Ctss -12.829632 -4.522893 0.0000000 0.0000000
494 C1qa -7.416728 -3.832811 0.0000000 0.0000000
493 Tmem119 -6.366945 -3.800780 0.0000000 0.0000000
470 Ccdc153 -2.569087 -3.144938 0.0101967 0.0401444
495 Inpp5d -7.445282 -2.828421 0.0000000 0.0000000
492 Cx3cr1 -5.666165 -2.750329 0.0000000 0.0000001
1 Syp 14.604422 2.616693 0.0000000 0.0000000
491 Trem2 -5.078127 -2.560248 0.0000004 0.0000034
498 Apoe -12.014446 -2.503629 0.0000000 0.0000000
480 Siglech -3.225496 -2.325987 0.0012575 0.0066891
61 Bsg 3.832298 1.912956 0.0001270 0.0008138
28 Gfap 6.662101 1.887792 0.0000000 0.0000000
0 Camk2a 16.020320 1.604297 0.0000000 0.0000000
7 Ptk2b 9.662978 1.584093 0.0000000 0.0000000
19 Nptx1 8.224086 1.530522 0.0000000 0.0000000
4 Slc17a7 11.085380 1.456908 0.0000000 0.0000000
488 Plcg2 -4.409460 -1.430689 0.0000104 0.0000773
477 Pdgfra -2.751270 -1.365383 0.0059365 0.0262676
472 Folr1 -2.639988 -1.289205 0.0082909 0.0342599
6 Grin1 10.691108 1.288557 0.0000000 0.0000000
487 Ppp1r1b -4.263815 -1.284282 0.0000201 0.0001456
87 Klf4 2.776866 1.207321 0.0054886 0.0249481
82 Klf2 2.889777 1.203468 0.0038552 0.0185344
10 Dnm1 9.490662 1.200793 0.0000000 0.0000000
21 Cpne6 7.658239 1.175915 0.0000000 0.0000000
27 Nr4a1 6.812413 1.135059 0.0000000 0.0000000
26 Dkk3 6.874430 1.044996 0.0000000 0.0000000
29 Zbtb20 6.594520 1.034572 0.0000000 0.0000000
24 Vgf 6.904668 1.012222 0.0000000 0.0000000

6.1.3 Control only, APP v.s. C6

Cell number compare: ‘APP’: 7121 ; ‘C6’: 9136

## [1] 7121
## [1] 9136

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
495 Plp1 -8.300681 -6.447118 0.0000000 0.0000000
70 App 6.985622 4.658610 0.0000000 0.0000000
12 Egr1 18.427420 3.835128 0.0000000 0.0000000
10 Grin1 18.693602 3.700864 0.0000000 0.0000000
487 Prkcd -6.147834 -2.912895 0.0000000 0.0000000
3 Slc17a7 21.532150 2.850603 0.0000000 0.0000000
0 Camk2a 30.099354 2.789707 0.0000000 0.0000000
9 Ptk2b 18.825884 2.732910 0.0000000 0.0000000
7 Nptx1 19.462187 2.729362 0.0000000 0.0000000
2 Nptxr 23.599588 2.588226 0.0000000 0.0000000
14 Dnm1 17.780014 2.525539 0.0000000 0.0000000
1 Dlg4 24.022236 2.403585 0.0000000 0.0000000
6 Grin2a 19.557583 2.368127 0.0000000 0.0000000
21 Syp 14.829331 2.209733 0.0000000 0.0000000
44 Nr4a2 9.675894 2.202026 0.0000000 0.0000000
4 Syngap1 20.664804 2.169545 0.0000000 0.0000000
488 Agt -6.226850 -2.138840 0.0000000 0.0000000
497 Apoe -9.418557 -2.085650 0.0000000 0.0000000
5 Grin2b 20.256319 2.083073 0.0000000 0.0000000
499 Gfap -16.051336 -2.063672 0.0000000 0.0000000
485 Synpo2 -4.845045 -2.053212 0.0000013 0.0000054
27 Nr4a1 13.733349 1.992821 0.0000000 0.0000000
20 Arc 14.955062 1.929970 0.0000000 0.0000000
494 Tcf7l2 -8.215328 -1.911108 0.0000000 0.0000000
59 Cckbr 8.238744 1.870255 0.0000000 0.0000000
498 C4b -12.261373 -1.860676 0.0000000 0.0000000
19 Hpca 16.044706 1.853020 0.0000000 0.0000000
15 Gria2 17.615229 1.823955 0.0000000 0.0000000
133 Rspo1 3.309680 1.770562 0.0009340 0.0030130
26 Vgf 14.196186 1.742860 0.0000000 0.0000000
38 Gria1 11.446211 1.620269 0.0000000 0.0000000
8 Rbfox3 18.889765 1.608638 0.0000000 0.0000000
18 Cx3cl1 16.199612 1.591508 0.0000000 0.0000000
13 Syn1 18.047415 1.565465 0.0000000 0.0000000
489 Enpp2 -6.433960 -1.483180 0.0000000 0.0000000
11 Fam131a 18.445550 1.470913 0.0000000 0.0000000
16 Slc30a3 17.169088 1.469251 0.0000000 0.0000000
30 Camk4 13.056713 1.399566 0.0000000 0.0000000
22 Rph3a 14.591459 1.344638 0.0000000 0.0000000
25 Dkk3 14.273308 1.343871 0.0000000 0.0000000
60 Zbtb20 8.227408 1.327582 0.0000000 0.0000000
84 Nptx2 5.746940 1.290526 0.0000000 0.0000000
91 Fosb 5.356630 1.254899 0.0000001 0.0000004
78 Plcxd2 6.373752 1.230456 0.0000000 0.0000000
131 Krt73 3.381140 1.216898 0.0007219 0.0023590
155 Pf4 2.591592 1.216042 0.0095533 0.0259601
132 Cux2 3.340073 1.214608 0.0008376 0.0027194
80 Lamp5 6.292746 1.208978 0.0000000 0.0000000
156 Col11a1 2.537400 1.204545 0.0111679 0.0301836
41 Tbr1 10.809135 1.203883 0.0000000 0.0000000
31 Cpne6 12.727281 1.181772 0.0000000 0.0000000
24 Smad3 14.521547 1.135137 0.0000000 0.0000000
23 Brinp1 14.580751 1.133443 0.0000000 0.0000000
119 Col6a1 4.020768 1.128259 0.0000580 0.0002117
87 Lrrc55 5.482105 1.082896 0.0000000 0.0000002
102 Igfbp6 4.866201 1.071764 0.0000011 0.0000049
71 Chrm4 6.935808 1.067390 0.0000000 0.0000000
96 Ccl6 5.152690 1.045405 0.0000003 0.0000012
151 Pten 2.766725 1.041025 0.0056622 0.0158163
17 Pcdhgc5 16.407131 1.018808 0.0000000 0.0000000
54 Rasgrf2 8.745890 1.013341 0.0000000 0.0000000
29 Dclk3 13.192946 1.006109 0.0000000 0.0000000

6.1.4 PLX only, APP v.s. C6

Cell number compare: ‘APP’: 4264 ; ‘C6’: 7781

## [1] 4264
## [1] 7781

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
497 App -13.880145 -9.670342 0.0000000 0.0000000
6 Penk 9.019672 4.652274 0.0000000 0.0000000
494 Prkcd -10.935171 -4.382350 0.0000000 0.0000000
0 Ppp1r1b 13.985020 4.381724 0.0000000 0.0000000
7 Adora2a 8.980073 4.121275 0.0000000 0.0000000
454 Calb2 -5.245508 -3.326567 0.0000002 0.0000011
473 Plp1 -7.015121 -3.178985 0.0000000 0.0000000
480 Synpo2 -7.919139 -3.133509 0.0000000 0.0000000
492 Syp -10.453685 -2.940215 0.0000000 0.0000000
8 Six3 8.773899 2.876801 0.0000000 0.0000000
493 Tcf7l2 -10.567602 -2.757150 0.0000000 0.0000000
22 Drd2 5.490453 2.562328 0.0000000 0.0000003
14 Scn4b 7.123028 2.416922 0.0000000 0.0000000
24 Otof 4.905724 2.416332 0.0000009 0.0000063
36 Clic6 3.680038 2.291078 0.0002332 0.0011320
3 Meis2 10.328524 2.274700 0.0000000 0.0000000
4 Syndig1l 10.225938 2.209832 0.0000000 0.0000000
425 Gfap -3.227096 -2.203738 0.0012505 0.0053902
489 Apoe -9.520561 -2.018902 0.0000000 0.0000000
487 Slc17a7 -9.024788 -1.932678 0.0000000 0.0000000
495 Plekhg1 -12.166815 -1.930067 0.0000000 0.0000000
499 Mapt -15.768661 -1.908040 0.0000000 0.0000000
436 Agt -3.768015 -1.868096 0.0001646 0.0008311
16 Drd1 6.816484 1.840841 0.0000000 0.0000000
498 Bin1 -14.733479 -1.773697 0.0000000 0.0000000
486 Dkk3 -9.008285 -1.729258 0.0000000 0.0000000
464 Cldn11 -5.949452 -1.651317 0.0000000 0.0000000
13 Syt6 7.184234 1.627475 0.0000000 0.0000000
490 Bsg -9.645227 -1.616300 0.0000000 0.0000000
470 Lef1 -6.515151 -1.534849 0.0000000 0.0000000
496 Cck -12.275343 -1.471486 0.0000000 0.0000000
403 Klf4 -2.506705 -1.366731 0.0121862 0.0414498
450 Sox10 -4.795091 -1.358600 0.0000016 0.0000108
462 Vgf -5.818213 -1.304803 0.0000000 0.0000001
455 Fibcd1 -5.276342 -1.271177 0.0000001 0.0000010
485 Adgra1 -8.345139 -1.270859 0.0000000 0.0000000
444 Dnm1 -3.965817 -1.247372 0.0000731 0.0004109
467 Eno2 -6.191310 -1.209307 0.0000000 0.0000000
474 Ptpru -7.086030 -1.188152 0.0000000 0.0000000
439 Mfsd2a -3.824056 -1.120665 0.0001313 0.0006983
448 Cbs -4.523027 -1.065574 0.0000061 0.0000396
38 Col6a1 3.551789 1.063238 0.0003826 0.0017714
12 Gng8 7.319304 1.035783 0.0000000 0.0000000
468 Camk2a -6.252263 -1.015054 0.0000000 0.0000000
483 Olig1 -8.127840 -1.014377 0.0000000 0.0000000
472 Enpp2 -6.950093 -1.007070 0.0000000 0.0000000
431 Gm2115 -3.571424 -1.003885 0.0003550 0.0016591
422 Ntng1 -3.125486 -1.002546 0.0017751 0.0074585

6.2 APP only, PLX v.s. control

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

6.2.1 CA1-ProS

Cell number compare: ‘PLX’: 767 ; ‘Control’: 308

## [1] 767
## [1] 308

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
453 App -3.790594 -8.404049 0.0001503 0.0015655
484 Hpca -5.712616 -7.086289 0.0000000 0.0000003
472 Grin1 -4.930967 -4.880014 0.0000008 0.0000146
499 Wfs1 -8.801627 -4.490318 0.0000000 0.0000000
480 Gria1 -5.209080 -4.333184 0.0000002 0.0000047
496 Egr1 -7.397917 -4.266816 0.0000000 0.0000000
493 Camk2a -6.812467 -3.609195 0.0000000 0.0000000
474 Grin2a -5.065786 -3.468377 0.0000004 0.0000078
471 Slc17a7 -4.913042 -3.412647 0.0000009 0.0000155
483 Dnm1 -5.587031 -3.291272 0.0000000 0.0000007
485 Syngap1 -5.838311 -2.977462 0.0000000 0.0000002
498 Adgrl2 -8.646818 -2.619645 0.0000000 0.0000000
490 Kcnab1 -6.147386 -2.514546 0.0000000 0.0000000
464 Dkk3 -4.318792 -2.441522 0.0000157 0.0002179
497 Gm2115 -7.662667 -2.386542 0.0000000 0.0000000
467 Fam131a -4.635037 -2.316480 0.0000036 0.0000541
473 Dlg4 -5.046449 -2.304920 0.0000005 0.0000083
444 Ptk2b -2.988303 -2.287666 0.0028053 0.0246080
462 Grin2b -4.225038 -2.073683 0.0000239 0.0003143
487 Brinp1 -6.024516 -2.026201 0.0000000 0.0000001
486 Cx3cl1 -5.845807 -1.972603 0.0000000 0.0000002
494 Plxna1 -6.875477 -1.958254 0.0000000 0.0000000
469 Fezf2 -4.817223 -1.814493 0.0000015 0.0000235
452 Gria2 -3.687388 -1.800285 0.0002266 0.0023119
488 Vgf -6.063082 -1.787795 0.0000000 0.0000001
451 Cpne6 -3.669137 -1.729893 0.0002434 0.0024337
479 Arc -5.175402 -1.725534 0.0000002 0.0000054
495 Bcan -6.943049 -1.724560 0.0000000 0.0000000
489 Epha10 -6.107842 -1.691080 0.0000000 0.0000000
476 Nr4a1 -5.087840 -1.655490 0.0000004 0.0000073
465 Nptx2 -4.402769 -1.585457 0.0000107 0.0001527
492 Ptpru -6.714150 -1.518369 0.0000000 0.0000000
445 Pthlh -3.007206 -1.448499 0.0026366 0.0235411
466 Plekhg1 -4.480988 -1.426212 0.0000074 0.0001093
491 Pkp2 -6.250157 -1.417509 0.0000000 0.0000000
450 Eno2 -3.643282 -1.297289 0.0002692 0.0026391
481 Sorl1 -5.358457 -1.292561 0.0000001 0.0000022
454 Bin1 -3.840568 -1.265778 0.0001228 0.0013059
468 Slc30a3 -4.740199 -1.238509 0.0000021 0.0000334
0 Gfap 4.052738 1.222129 0.0000506 0.0006173
446 Nr4a2 -3.032954 -1.144256 0.0024217 0.0220157
478 Robo1 -5.153566 -1.139854 0.0000003 0.0000058
482 Cck -5.390831 -1.120382 0.0000001 0.0000019
440 Sulf2 -2.837188 -1.081264 0.0045513 0.0373056
463 Gria3 -4.286744 -1.071109 0.0000181 0.0002450
441 Mink1 -2.892919 -1.029978 0.0038168 0.0318066
459 Syn1 -3.971585 -1.005008 0.0000714 0.0008500

6.2.2 CA2

Cell number compare: ‘PLX’: 80 ; ‘Control’: 134.

## [1] 80
## [1] 134

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
499 Zbtb20 -4.593225 -6.402827 0.0000044 0.0021822
498 Gria1 -3.936073 -4.788919 0.0000828 0.0207065
496 Syngap1 -3.703331 -3.032099 0.0002128 0.0265984
497 Mapt -3.742121 -1.788793 0.0001825 0.0265984

6.2.3 CA3

Cell number compare: ‘PLX’: 397 ; ‘Control’: 425.

## [1] 397
## [1] 425

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
488 Slc17a7 -3.531298 -3.199179 0.0004135 0.0159048
498 Gria1 -4.536818 -3.075956 0.0000057 0.0009518
497 Ptk2b -4.382925 -3.067826 0.0000117 0.0014637
490 Zbtb20 -3.716792 -2.313827 0.0002018 0.0091713
495 Syngap1 -4.102038 -1.647356 0.0000410 0.0034127
494 Camk2a -3.992094 -1.639011 0.0000655 0.0045413
0 Gfap 4.927943 1.520422 0.0000008 0.0004155
486 Dlg4 -3.232332 -1.368185 0.0012278 0.0409281
489 Grm2 -3.651531 -1.106893 0.0002607 0.0108617
493 Itga7 -3.967401 -1.072866 0.0000727 0.0045413
492 Slc30a3 -3.898465 -1.043471 0.0000968 0.0053780
487 Brinp1 -3.368145 -1.028354 0.0007568 0.0270270

6.2.4 DG

Cell number compare: ‘PLX’: 97 ; ‘Control’: 143

## [1] 97
## [1] 143

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

6.3 C6 only, PLX v.s. control

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

6.3.1 CA1-ProS

Cell number compare: ‘PLX’: 631 ; ‘Control’: 782

## [1] 631
## [1] 782

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
3 App 5.790393 12.891213 0.0000000 0.0000009
5 Ptk2b 5.396896 3.497551 0.0000001 0.0000048
0 Camk2a 7.807320 3.118698 0.0000000 0.0000000
2 Zbtb20 6.761383 2.588190 0.0000000 0.0000000
17 Nptx1 3.678650 2.354456 0.0002345 0.0058618
13 Syp 3.957265 2.335203 0.0000758 0.0023691
22 Grin1 3.002997 2.255974 0.0026734 0.0495065
4 Cpne6 5.597284 2.194341 0.0000000 0.0000018
15 Fibcd1 3.877071 1.937821 0.0001057 0.0029367
10 Nr4a2 4.180668 1.776978 0.0000291 0.0011179
1 Nefm 7.410151 1.633473 0.0000000 0.0000000
6 Bin1 4.788848 1.231143 0.0000017 0.0000932
498 Adgrl2 -5.072906 -1.074066 0.0000004 0.0000245
14 Nptxr 3.909660 1.073459 0.0000924 0.0027184
499 Bcan -5.636889 -1.030305 0.0000000 0.0000017

6.3.2 CA2

Cell number compare: ‘PLX’: 117 ; ‘Control’: 118.

## [1] 117
## [1] 118

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

6.3.3 CA3

Cell number compare: ‘PLX’: 896 ; ‘Control’: 486 .

## [1] 896
## [1] 486

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
6 App 5.988654 12.676558 0.0000000 0.0000001
2 Col6a1 7.440753 7.732464 0.0000000 0.0000000
3 Plagl1 7.309687 5.100309 0.0000000 0.0000000
12 Syp 4.902721 4.119861 0.0000009 0.0000315
5 Nptxr 6.027261 3.850422 0.0000000 0.0000001
23 Nptx1 3.806060 3.482384 0.0001412 0.0024345
16 Cpne6 4.522863 3.188512 0.0000061 0.0001525
1 Nr2f2 7.861829 3.170705 0.0000000 0.0000000
9 Zbtb20 5.425078 2.983680 0.0000001 0.0000024
4 Nnat 7.298112 2.638367 0.0000000 0.0000000
0 Crtac1 8.777737 2.481828 0.0000000 0.0000000
15 Tcerg1l 4.682373 2.331260 0.0000028 0.0000746
11 Fosl2 4.998215 2.150707 0.0000006 0.0000207
37 Col5a2 2.900386 1.911841 0.0037270 0.0404421
8 Adgra1 5.431007 1.688240 0.0000001 0.0000024
497 Brinp1 -4.684701 -1.567339 0.0000028 0.0000746
10 Fezf2 5.063077 1.438733 0.0000004 0.0000159
27 Eno2 3.582112 1.423155 0.0003408 0.0050122
26 Ptpru 3.591781 1.403387 0.0003284 0.0049761
20 Bin1 4.233982 1.357217 0.0000230 0.0004783
31 Rspo2 3.264999 1.326645 0.0010946 0.0144032
18 Syt17 4.318748 1.322203 0.0000157 0.0003507
13 Cnr1 4.840188 1.249465 0.0000013 0.0000405
22 Dlg4 3.877839 1.233872 0.0001054 0.0018819
34 Dkk3 3.054461 1.182020 0.0022547 0.0262169
7 Kit 5.462627 1.169676 0.0000000 0.0000023
17 Mink1 4.349097 1.119043 0.0000137 0.0003255
495 Bcan -3.988084 -1.110037 0.0000666 0.0012335
492 Fam131a -3.064624 -1.071578 0.0021794 0.0259457
24 Cplx1 3.787991 1.063867 0.0001519 0.0025312
498 Epha7 -6.492026 -1.017116 0.0000000 0.0000000

6.3.4 DG

Cell number compare: ‘PLX’: 145 ; ‘Control’: 102

## [1] 145
## [1] 102

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
499 Hpca -4.845665 -4.467802 1.30e-06 0.0006309
498 Nefm -4.325647 -2.383967 1.52e-05 0.0038021

6.4 PLX only, APP v.s. C6

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

6.4.1 CA1-ProS

Cell number compare: ‘APP’: 782 ; ‘C6’: 308

## [1] 782
## [1] 308

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
486 App -3.770907 -9.130591 0.0001627 0.0058091
487 Dkk3 -3.893462 -3.569085 0.0000988 0.0038009
490 Ptk2b -3.991229 -3.138422 0.0000657 0.0030493
498 Kcnab1 -5.636379 -2.779752 0.0000000 0.0000043
491 Egr1 -4.484122 -2.677108 0.0000073 0.0004067
497 Camk2a -5.035248 -2.604655 0.0000005 0.0000740
475 Slc17a7 -3.094340 -2.199769 0.0019725 0.0394502
488 Syngap1 -3.965692 -1.918197 0.0000732 0.0030493
495 Wfs1 -4.780948 -1.859754 0.0000017 0.0001745
477 Cpne6 -3.162617 -1.731729 0.0015636 0.0339909
499 Ptpru -5.858304 -1.600056 0.0000000 0.0000023
494 Gm2115 -4.734789 -1.563882 0.0000022 0.0001827
480 Fezf2 -3.289980 -1.553409 0.0010019 0.0250486
489 Fibcd1 -3.970393 -1.508155 0.0000718 0.0030493
483 Nr4a2 -3.604116 -1.466884 0.0003132 0.0092123
482 Eno2 -3.514683 -1.357158 0.0004403 0.0122300
481 Bin1 -3.483804 -1.201917 0.0004943 0.0130090
493 Cck -4.631894 -1.159318 0.0000036 0.0002588
492 Pkp2 -4.495555 -1.100752 0.0000069 0.0004067
476 Arc -3.120198 -1.069206 0.0018073 0.0376520
484 Cx3cl1 -3.613625 -1.068221 0.0003019 0.0092123

6.4.2 CA2

Cell number compare: ‘APP’: 80 ; ‘C6’: 117.

## [1] 80
## [1] 117

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

6.4.3 CA3

Cell number compare: ‘APP’: 397 ; ‘C6’: 896.

## [1] 397
## [1] 896

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
497 App -7.835498 -15.362594 0.0000000 0.0000000
496 Col6a1 -7.786898 -9.011167 0.0000000 0.0000000
495 Syp -7.782215 -6.274181 0.0000000 0.0000000
494 Plagl1 -7.692765 -5.432734 0.0000000 0.0000000
481 Slc17a7 -5.761420 -5.392075 0.0000000 0.0000002
489 Gria1 -6.725518 -4.194874 0.0000000 0.0000000
479 Cpne6 -5.430500 -3.738366 0.0000001 0.0000013
484 Nptxr -5.961231 -3.659163 0.0000000 0.0000001
492 Nr2f2 -6.948338 -3.652885 0.0000000 0.0000000
477 Ptk2b -5.365188 -3.382440 0.0000001 0.0000018
488 Zbtb20 -6.275761 -3.091775 0.0000000 0.0000000
471 Tcerg1l -5.019657 -3.009680 0.0000005 0.0000089
498 Eno2 -7.994298 -2.813303 0.0000000 0.0000000
451 Hpca -3.295550 -2.758693 0.0009823 0.0091032
499 Crtac1 -8.839882 -2.670600 0.0000000 0.0000000
443 Col5a2 -3.046008 -2.446339 0.0023190 0.0190083
490 Bin1 -6.795108 -2.402109 0.0000000 0.0000000
463 Ptpru -4.331661 -2.399196 0.0000148 0.0001897
486 Nnat -6.038895 -2.376615 0.0000000 0.0000001
456 Calb2 -3.747809 -2.271042 0.0001784 0.0018977
493 Sulf2 -7.190452 -2.213496 0.0000000 0.0000000
480 Syngap1 -5.443014 -2.063145 0.0000001 0.0000013
473 Fosl2 -5.076895 -1.972176 0.0000004 0.0000071
487 Adgra1 -6.107032 -1.923982 0.0000000 0.0000000
462 Camk2a -4.322134 -1.801131 0.0000155 0.0001932
482 Plxna1 -5.791290 -1.762644 0.0000000 0.0000002
474 Vgf -5.162310 -1.751491 0.0000002 0.0000047
461 Dkk3 -4.254239 -1.733265 0.0000210 0.0002558
470 Dlg4 -4.958462 -1.678501 0.0000007 0.0000118
467 Fam107a -4.798694 -1.630923 0.0000016 0.0000242
466 Fezf2 -4.604373 -1.484388 0.0000041 0.0000608
459 Gria2 -4.013981 -1.484091 0.0000597 0.0006942
476 Cnr1 -5.238116 -1.446475 0.0000002 0.0000034
468 Cplx1 -4.833812 -1.420296 0.0000013 0.0000209
478 Mas1 -5.408137 -1.404513 0.0000001 0.0000014
491 Bsg -6.816099 -1.372706 0.0000000 0.0000000
485 Neto1 -5.993039 -1.369099 0.0000000 0.0000001
483 Cck -5.833997 -1.290572 0.0000000 0.0000002
469 Mapt -4.885723 -1.212052 0.0000010 0.0000166
472 Syn1 -5.041131 -1.208403 0.0000005 0.0000083
0 Dclk3 4.588468 1.134732 0.0000045 0.0000638
458 Mink1 -3.891834 -1.115539 0.0000995 0.0011054
440 Hcn1 -2.906746 -1.103341 0.0036521 0.0280931
475 Camk4 -5.188063 -1.063567 0.0000002 0.0000042
449 Nefm -3.262853 -1.062377 0.0011030 0.0100270

6.4.4 DG

Cell number compare: ‘APP’: 97 ; ‘C6’: 145

## [1] 97
## [1] 145

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

6.5 Control only, APP v.s. C6

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

6.5.1 CA1-ProS

Cell number compare: ‘APP’: 631 ; ‘C6’: 767

## [1] 631
## [1] 767

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
8 App 5.781549 12.164670 0.0000000 0.0000004
6 Grin1 6.183330 5.227798 0.0000000 0.0000000
0 Camk2a 10.005967 4.123237 0.0000000 0.0000000
3 Grin2a 7.332690 4.090010 0.0000000 0.0000000
15 Egr1 5.379902 3.774128 0.0000001 0.0000023
38 Gria1 3.939990 3.099695 0.0000815 0.0010447
1 Zbtb20 7.940286 3.059491 0.0000000 0.0000000
2 Grin2b 7.342675 2.918111 0.0000000 0.0000000
12 Dnm1 5.535995 2.691057 0.0000000 0.0000012
35 Ptk2b 4.026789 2.646795 0.0000565 0.0007853
7 Nr4a1 5.904626 2.390820 0.0000000 0.0000002
11 Gria2 5.614274 2.240807 0.0000000 0.0000008
5 Cpne6 6.198639 2.192505 0.0000000 0.0000000
43 Syp 3.662617 2.026821 0.0002497 0.0028369
13 Dlg4 5.447664 1.948673 0.0000001 0.0000018
24 Syngap1 4.567688 1.936160 0.0000049 0.0000986
32 Arc 4.125836 1.809557 0.0000369 0.0005597
57 Wfs1 3.183090 1.780875 0.0014571 0.0125614
10 Brinp1 5.710459 1.653508 0.0000000 0.0000005
4 Nptxr 6.339089 1.559325 0.0000000 0.0000000
26 Vgf 4.515103 1.455290 0.0000063 0.0001172
48 Nr4a2 3.444421 1.454350 0.0005723 0.0058396
47 Fam131a 3.448548 1.407428 0.0005636 0.0058396
21 Gm2115 4.696423 1.405113 0.0000026 0.0000602
17 Bin1 5.228735 1.295003 0.0000002 0.0000047
25 Mink1 4.520494 1.203446 0.0000062 0.0001172
41 Cx3cl1 3.697697 1.134877 0.0002176 0.0025901
22 Itga7 4.639245 1.128132 0.0000035 0.0000759
30 Rbfox3 4.291780 1.117081 0.0000177 0.0002859
27 Epha10 4.463782 1.086565 0.0000081 0.0001411
9 Robo1 5.722574 1.075899 0.0000000 0.0000005
16 Crhr1 5.349482 1.002607 0.0000001 0.0000026

6.5.2 CA2

Cell number compare: ‘APP’: 134 ; ‘C6’: 118.

## [1] 134
## [1] 118

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Zbtb20 3.913356 4.014938 9.1e-05 0.0455112

6.5.3 CA3

Cell number compare: ‘APP’: 425 ; ‘C6’: 486

## [1] 425
## [1] 486

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
1 Nptx1 3.908714 2.874441 9.28e-05 0.0115986
498 Sulf2 -4.217771 -1.168880 2.47e-05 0.0041121
0 Smad3 4.683566 1.105830 2.80e-06 0.0014096

6.5.4 DG

Cell number compare: ‘APP’: 143 ; ‘C6’: 102

## [1] 143
## [1] 102

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

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Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic